barriers − Compute local minima and energy barriers of a landscape
barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt. For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory.
accepts the following options:
-q, --quiet, --silent
be quiet, don’t do PostScript output.
Print more information.
Show summary of options.
Show version of program.
Print the size of of each basin in output.
compute only the lowest num local minima.
print only minima with energy barrier greater than delta (default 0)
print the saddle point conformations in output
compute rates between macro states (basins) for use with treekin
Set temperature in centigrade. Used to compute Boltzmann fators in conjunction with --rates. (default = 37)
input landscape is a poset with n objective functions
Compute a minimal barrier path between local minima l1 and l2. The result will be written to the file "path.l1.l2.txt"
Set the type of configuration
space, where graph can be one of:
|RNA||RNA secondary structures (default)|
|RNA-noLP||canonical RNA structures (i.e. without isolated pairs)|
|Q2||Spin glass (strings of "+-")|
|Qa||a-letter hamming graph (e.g. Q3 strings of "ABC").|
|T||Phylogenetic Trees in bracket notation, e.g.|
|P||Permutations (as comma separated list), e.g.|
The type of landscape may also
be set by the input file using the fourth word on first
AUCGUGAGCUGUGUAGCUUAGCUAGCUAGC -610 100 :: RNA-noLP
for an landscape of canonical RNA structures
Set the moveset for generating neighbors of a configuration. For RNA possible values are Shift (default) or noShift. For Permutations possibilities are, T for transpositions (default), C for canonical transpositions, and R for reversal moves. Spin Glass always uses point mutations (single spin flip), Trees use NNI (Nearest Neighbour Interchange).
Ivo Hofacker, Christoph Flamm, Peter Stadler. Send comments to firstname.lastname@example.org.